DNA copy number alterations are one of the many causes which affect gene expression alterations. In recent years, comprehensive search methods using such as array CGH have been employed in the analysis of DNA copy numbers, and such methods have been gradually demonstrated to be useful. An epoch-making article which identified the causative gene for melanoma drug resistance from analyses of NCI60 screening panel cell lines with 100K SNP arrays (Affymetrix) was published in Nature in July last year (Non-Patent Document 1). The raw data contained in the article are disclosed in NCI database and invite re-analysis by the third party. On the other hand, no report has been made about correlation between abnormalities in DNA copy numbers and the efficacies of existing anticancer agents.
To date, as a method for predicting sensitivities to 5-fluorouracil-based anticancer agents, determination of the enzyme activity of dihydropyrimidine dehydrogenase prepared from a cancer cell line or cancer tissue, determination of the quantity thereof by ELISA, or determination of its mRNA expression level has been attempted (Non-Patent Documents 2 and 3, Patent Document 1). However, enzyme or mRNA is easily degraded when fresh tissues from surgical operation are stored. Yet, the degree of degradation varies depending on the laboratory. Thus, it has been difficult to use the enzyme activity, quantity or mRNA expression level as a common indicator for predicting sensitivity. Furthermore, a large amount of tissue is required for determination of enzyme activity, and the amount of sample obtainable from biopsy or the like was insufficient to enable such determination. Besides, determination of mRNA expression levels using paraffin-embedded samples which are widely used in histopathology is difficult in terms of maneuver.    [Non-Patent Document 1]Integrative genomic analyses identify MITF as a lineage survival oncogene amplified in malignant melanoma: Garraway-L A, et al. Nature (2005) vol. 436, 7 July, pp 117-121    [Non-Patent Document 2]Dihydropyrimidine dehydrogenase activity in human peripheral blood mononuclear cells and liver; population characteristics, newly identified deficient patients, and clinical implication in 5-fluorouracil chemotherapy: Lu Z, Zhang R, Diasio R B. Cancer Res. 1993 Nov. 15; 53(22):5433-8    [Non-Patent Document 3]A role for dihydropyrimidine dehydrogenase and thymidylate synthase in tumour sensitivity to fluorouracil: Beck A, Etienne M C, Cheradame S, Fischel J L, Formento P, Renee N, Milano G. Eur J Cancer. 1994; 30A(10): 1517-22    [Patent Document 1]Japanese Unexamined Patent Publication (PCT) No. 2005-508603